Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component (characterized)
to candidate AZOBR_RS08655 AZOBR_RS08655 amino acid ABC transporter substrate-binding protein
Query= reanno::Smeli:SMc02118 (341 letters) >FitnessBrowser__azobra:AZOBR_RS08655 Length = 340 Score = 456 bits (1173), Expect = e-133 Identities = 219/342 (64%), Positives = 262/342 (76%), Gaps = 3/342 (0%) Query: 1 MARRILTALVGAAVVGIGTHAASAATLDDVKAKGFVQCGVNTGLAGFAAPDASGNWSGFD 60 M IL A A V G T A + TLD VK +GFVQCGVN GL GF PD+SGNW+G D Sbjct: 1 MKSGILAAAAAAVVFGAVTGAQAGPTLDAVKGRGFVQCGVNAGLPGFGNPDSSGNWTGLD 60 Query: 61 VDYCKAIAAAIFGDGSKVKYTPLSAKERFPALQSGEVDVLARNTTWSINRDTALGFNFRP 120 VDYC+A+A A+F D +KVK+TPLSA++RFPA+QSGEVD+L+RNTT ++ RDT++G NF P Sbjct: 61 VDYCRAVAVALFNDPNKVKFTPLSAQQRFPAIQSGEVDLLSRNTTVTLTRDTSVGLNFAP 120 Query: 121 VNYYDGQGFMVRKELDVKSALELSGAAVCVQTGTTTELNLADYFKANNLQYNPVVFEKLE 180 V YYDGQGFMV K+L VKSA EL+GA VCVQ GTTTELNLADYF+ NN+ YNPVV E + Sbjct: 121 VTYYDGQGFMVNKKLGVKSAKELNGATVCVQAGTTTELNLADYFRTNNMSYNPVVIESND 180 Query: 181 EVNAAYDAGRCDVYTTDQSGLYSLRLTLSK-PDDHIVLPEIISKEPLAPAVRQGDDQWFD 239 EVNAAY AGRCDV TTD SGL R ++ PDDHI+LPEIISKEPLAPAVR GDDQWFD Sbjct: 181 EVNAAYFAGRCDVLTTDASGLAGTRAGVAPVPDDHIILPEIISKEPLAPAVRHGDDQWFD 240 Query: 240 IVSWVHYALVQAEEFGVTQANLEEMKKSTNPDVQRFLGVEADSKIGTDLGLTNEWAVNIV 299 +V W YA +QAEE G+T N++E S NP++QR LG +G LGL +WA NI+ Sbjct: 241 VVKWTVYATIQAEEMGITSKNVDEFVNSKNPEIQRILGTSPG--MGKALGLDEKWAYNII 298 Query: 300 KAVGNYGEVFDRNIGAGSPLKIERGLNALWNKGGLQYAPPVR 341 K +GNYGE+F+RN+G +PLK+ERGLNALW GGLQYA P+R Sbjct: 299 KTMGNYGEIFERNVGTKTPLKLERGLNALWTNGGLQYAMPIR 340 Lambda K H 0.317 0.134 0.399 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 445 Number of extensions: 24 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 341 Length of database: 340 Length adjustment: 28 Effective length of query: 313 Effective length of database: 312 Effective search space: 97656 Effective search space used: 97656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory